compiler warnings: unused parameters

[peterjc]

Using Mac OS X 10.10.5,

$ uname
Darwin
$ g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.0 (clang-700.1.76)
Target: x86_64-apple-darwin14.5.0
Thread model: posix

Attempting to build the latest code for chopBAI, specifically commit 6dfdaa5 as follows:

$ git clone https://github.com/seqan/seqan.git
$ git clone https://github.com/DecodeGenetics/chopBAI.git
$ cd chopBAI
$ emacs Makefile
...
$ git diff
diff --git a/Makefile b/Makefile
index 24ec4fb..04eb225 100644
--- a/Makefile
+++ b/Makefile
@@ -4,7 +4,7 @@ CC=$(CXX)

 # Set this to include SeqAn libraries, either system wide
 # or download into current folder and set to .
-SEQAN_LIB=.
+SEQAN_LIB=../seqan/include/

 CXXFLAGS+=-I$(SEQAN_LIB) -DSEQAN_HAS_ZLIB=1
 LDLIBS=-lz -lpthread

Then compiling gives:

$ make
g++ -I../seqan/include/ -DSEQAN_HAS_ZLIB=1 -DDATE=\""on 2015-11-06 17:36:57"\" -W -Wall -Wno-long-long -pedantic -Wno-variadic-macros -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -Qunused-arguments  -c -o chopBAI.o chopBAI.cpp
In file included from chopBAI.cpp:7:
./bam_index_csi.h:173:55: warning: unused parameter 'bamFile' [-Wunused-parameter]
bool jumpToOrphans(FormattedFile<Bam, Input, TSpec> & bamFile,
                                                      ^
./bam_index_csi.h:174:27: warning: unused parameter 'hasAlignments' [-Wunused-parameter]
                   bool & hasAlignments,
                          ^
./bam_index_csi.h:175:42: warning: unused parameter 'index' [-Wunused-parameter]
                   BamIndex<Csi> const & index)
                                         ^
3 warnings generated.
g++   chopBAI.o  -lz -lpthread -o chopBAI

Compilation gives three warnings as shown above, but seems to work:

$ ./chopBAI --version
./chopBAI version 0.1 beta

[pmelsted]

Thanks for reporting this. The CSI format is not a part of SeqAn so we implemented something basic instead and kept the same API. The function jumpToOrphans, to find the unaligned readpairs in a BAM file is not used in the code and not implemented, but is just a stub. So even if clang complains about unused options the binary is still fine.

[peterjc]

Its good to hear this is a harmless warning, but can you not silence the warning in these cases? e.g. using a pragma or a void statement line inside the function (with an explanatory comment).

Having chopBAI compile without warnings would be a big improvement.